Genomic analysis of bacteria in the Acute Oak Decline pathobiome

The UK’s native oak is under serious threat from Acute Oak Decline (AOD). Stem tissue necrosis is a primary symptomof AOD and several bacteria are associated with necrotic lesions. Two members of the lesion pathobiome, Brenneriagoodwinii and Gibbsiella quercinecans, have been identified as causative agents of tissue necrosis. However, additionalbacteria including Lonsdalea britannica and Rahnella species have been detected in the lesion microbiome, but their rolein tissue degradation is unclear. Consequently, information on potential genome-encoded mechanisms for tissuenecrosis is critical to understand the role and mechanisms used by bacterial members of the lesion pathobiome in theaetiology of AOD. Here, the whole genomes of bacteria isolated from AOD-affected trees were sequenced, annotatedand compared against canonical bacterial phytopathogens and non-pathogenic symbionts. Using orthologous geneinference methods, shared virulence genes that retain the same function were identified. Furthermore, functionalannotation of phytopathogenic virulence genes demonstrated that all studied members of the AOD lesion microbiotapossessed genes associated with phytopathogens. However, the genome of B. goodwinii was the most characteristic ofa necrogenic phytopathogen, corroborating previous pathological and metatranscriptomic studies that implicate it as thekey causal agent of AOD lesions. Furthermore, we investigated the genome sequences of other AOD lesion microbiotato understand the potential ability of microbes to cause disease or contribute to pathogenic potential of organismsisolated from this complex pathobiome. The role of these members remains uncertain but some such as G.quercinecans may contribute to tissue necrosis through the release of necrotizing enzymes and may help moredangerous pathogens activate and realize their pathogenic potential or they may contribute as secondary/opportunisticpathogens with the potential to act as accessory species for B. goodwinii. We demonstrate that in combination withecological data, whole genome sequencing provides key insights into the pathogenic potential of bacterial specieswhether they be phytopathogens, part-contributors or stimulators of the pathobiome.